A thin-layer chromatographic study was made of the chloroform-soluble and flavonoid fractions from the fruit peels of 16 species, 2 varieties and 5 formas of the Citrus plants cultivated in Je Ju Island for their interspecific relatinships. In addition, 3 hybrids and 9 native plants were also studied for their taxonomic position. Three phenograms were developed from these chromatographic data after cluster analysis via the unweighted paired group method using rithmatic average by Sneath and Sokal. These plants were grouped into 5 alliences based on the phenogram obtained from the chloroform-soluble fracitons, which were nearly identical to the subgenus rank by Tanaka, and rutinoside and neohesperidoside groups by Horowitz. Those from the flavonoid and methanol-soluble fractions were not able to evaluate the morphological classification except for a few cases.